rcsb-mojave-tools
Used in:
components
- OverviewOverview
- VersionsVersions
- DependentsDependents
- DependenciesDependencies
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>rcsb-mojave-tools</artifactId>
<version>1.9.0</version>
</dependency><?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<packaging>jar</packaging>
<name>Mojave: JSON Schema Tools</name>
<description>Provides tools to work with JSON schemas.</description>
<url>https://github.com/rcsb/rcsb-mojave-tools</url>
<groupId>org.rcsb</groupId>
<artifactId>rcsb-mojave-tools</artifactId>
<version>1.9.0</version>
<!-- https://central.sonatype.org/pages/apache-maven.html -->
<!-- https://github.com/chhh/sonatype-ossrh-parent/blob/master/pom.xml -->
<distributionManagement>
<snapshotRepository>
<id>ossrh</id>
<url>https://oss.sonatype.org/content/repositories/snapshots</url>
</snapshotRepository>
<repository>
<id>ossrh</id>
<url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
</repository>
</distributionManagement>
<organization>
<name>RCSB PDB</name>
<url>https://www.rcsb.org/</url>
</organization>
<licenses>
<license>
<name>MIT License</name>
<url>https://opensource.org/license/mit/</url>
</license>
</licenses>
<developers>
<developer>
<name>Yana Rose</name>
<email>yana.rose@rcsb.org</email>
<organization>RCSB PDB</organization>
<organizationUrl>https://www.rcsb.org</organizationUrl>
</developer>
</developers>
<scm>
<url>https://github.com/rcsb/rcsb-mojave-tools</url>
<connection>scm:git:git://github.com/rcsb/rcsb-mojave-tools.git</connection>
<developerConnection>scm:git:git@github.com:rcsb/rcsb-mojave-tools.git</developerConnection>
<tag>1.9.0</tag>
</scm>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<!-- Configure package name for automatically generated models -->
<uniprot.auto.package>org.rcsb.uniprot.auto</uniprot.auto.package>
<ncbi.auto.package>org.rcsb.ncbi.auto</ncbi.auto.package>
<mesh.auto.package>org.rcsb.mesh.auto</mesh.auto.package>
<!-- DEPENDENCY VERSIONS -->
<jdk.version>11</jdk.version>
<junit.version>4.13.2</junit.version>
<slf4j.version>2.0.12</slf4j.version>
<log4j.version>2.23.1</log4j.version>
<jackson.version>2.13.3</jackson.version>
<swagger.version>2.2.0</swagger.version>
<jsonschema2pojo.version>1.1.2</jsonschema2pojo.version>
<pojo2jsonschema.version>1.16</pojo2jsonschema.version>
<bean.validation.api.version>2.0.1.Final</bean.validation.api.version>
<!-- SOURCES OF SCHEMAS FOR EXTERNAL DATA -->
<!-- uniprot -->
<uniprot.xsd.schema.source.url>https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/</uniprot.xsd.schema.source.url>
<uniprot.xsd.schema.name>uniprot.xsd</uniprot.xsd.schema.name>
<!-- NCBI esummary.fcgi xsd schema location -->
<ncbi.xsd.esummary.schema.file>src/main/resources/xsd-schemas/ncbi-esummary.xsd</ncbi.xsd.esummary.schema.file>
<ncbi.xsd.efetch.schema.file>src/main/resources/xsd-schemas/ncbi-efetch.xsd</ncbi.xsd.efetch.schema.file>
<!-- where we store downloaded XSD schema for uniprot -->
<uniprot.xsd.schema.download.location>generated-sources/xsd/uniprot</uniprot.xsd.schema.download.location>
<!-- where we store auto generated classes from XSD schema for uniprot -->
<uniprot.auto.gen.classes.location>generated-sources/xjc/uniprot</uniprot.auto.gen.classes.location>
<!-- where we store auto generated classes from XSD schema for NCBI esummary.fcgi -->
<ncbi.auto.gen.classes.location>generated-sources/xjc/ncbi</ncbi.auto.gen.classes.location>
<!-- where we store auto generated classes from DTD schema for MeSH terminology -->
<mesh.auto.gen.classes.location>generated-sources/xjc/mesh</mesh.auto.gen.classes.location>
</properties>
<dependencies>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-core</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- Used by jsonschema2pojo -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- Used by jsonschema2pojo -->
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-annotations</artifactId>
<version>${jackson.version}</version>
</dependency>
<!-- Used by jsonschema2pojo -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.12.0</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>33.1.0-jre</version>
</dependency>
<!-- Since java 11 JRE, this is needed at runtime (not in JRE anymore) -->
<dependency>
<groupId>jakarta.xml.bind</groupId>
<artifactId>jakarta.xml.bind-api</artifactId>
<version>4.0.1</version>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
<artifactId>jaxb-runtime</artifactId>
<version>4.0.5</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.openjdk.nashorn</groupId>
<artifactId>nashorn-core</artifactId>
<version>15.4</version>
</dependency>
<!-- Tool to generate DTO style Java classes from JSON schema -->
<dependency>
<groupId>org.jsonschema2pojo</groupId>
<artifactId>jsonschema2pojo-core</artifactId>
<version>${jsonschema2pojo.version}</version>
</dependency>
<!-- API annotations -->
<dependency>
<groupId>io.swagger.core.v3</groupId>
<artifactId>swagger-annotations</artifactId>
<version>${swagger.version}</version>
</dependency>
<!-- The validation api v2. Used to decorate generated POJOs so that annotations like @NotNull
work well with graphql-spqr. See TestGraphQLSchemaGenMojave in rcsb-yosemite -->
<dependency>
<groupId>javax.validation</groupId>
<artifactId>validation-api</artifactId>
<version>${bean.validation.api.version}</version>
</dependency>
<!-- API for Log4J -->
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>
<!-- Binding for Log4J, purely used for tests and for the CLI apps in this project: thus runtime scope -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-slf4j2-impl</artifactId>
<version>${log4j.version}</version>
<scope>runtime</scope>
</dependency>
<!-- Log4j API and Core implementation required for binding -->
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
<version>${log4j.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>${log4j.version}</version>
<scope>runtime</scope>
</dependency>
<!-- Testing dependencies -->
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
<scope>test</scope>
</dependency>
</dependencies>
<profiles>
<profile>
<id>sonar</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<properties>
<!-- Optional URL to server. Default value is http://localhost:9000 -->
<sonar.host.url>
http://sonarqube.rcsb.org
</sonar.host.url>
</properties>
</profile>
<profile>
<!-- A profile only to be used when releasing-->
<id>release</id>
<build>
<plugins>
<!-- handles propagating the build to the staging repository -->
<plugin>
<groupId>org.sonatype.plugins</groupId>
<artifactId>nexus-staging-maven-plugin</artifactId>
<version>1.6.13</version>
<extensions>true</extensions>
<configuration>
<serverId>ossrh</serverId>
<nexusUrl>https://oss.sonatype.org/</nexusUrl>
<autoReleaseAfterClose>true</autoReleaseAfterClose>
</configuration>
</plugin>
<!-- signing of content to be published -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>3.1.0</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
<configuration>
<!-- This is necessary for gpg to not try to use the pinentry programs -->
<gpgArguments>
<arg>--pinentry-mode</arg>
<arg>loopback</arg>
</gpgArguments>
</configuration>
</execution>
</executions>
</plugin>
<!-- create source -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>3.3.0</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<!-- create javadoc -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.6.3</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
<configuration>
<!-- so that javadoc generator is not so strict about missing docs -->
<!-- https://stackoverflow.com/questions/15886209/maven-is-not-working-in-java-8-when-javadoc-tags-are-incomplete -->
<doclint>none</doclint>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.7.0</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
</plugin>
<!-- https://mvnrepository.com/artifact/org.sonarsource.scanner.maven/sonar-maven-plugin -->
<plugin>
<groupId>org.sonarsource.scanner.maven</groupId>
<artifactId>sonar-maven-plugin</artifactId>
<version>3.2</version>
</plugin>
<!-- Write project properties file at build time -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
<version>1.0.0</version>
<executions>
<execution>
<phase>generate-resources</phase>
<goals>
<goal>write-project-properties</goal>
</goals>
<configuration>
<outputFile>${basedir}/src/main/resources/tools.module.properties</outputFile>
</configuration>
</execution>
</executions>
</plugin>
<!-- Downloads files in part of maven build -->
<plugin>
<groupId>com.googlecode.maven-download-plugin</groupId>
<artifactId>download-maven-plugin</artifactId>
<version>1.3.0</version>
<configuration>
<!-- plugin is caching the downloaded file, getting it from .m2 folder. When skipping cache
the file will be downloaded every time maven runs (needed because the file may change) -->
<skipCache>true</skipCache>
</configuration>
<executions>
<!-- UniProt KB -->
<execution>
<!-- the wget goal actually binds itself to this phase by default -->
<phase>initialize</phase>
<id>download-uniprot-schema</id>
<goals>
<goal>wget</goal>
</goals>
<configuration>
<url>${uniprot.xsd.schema.source.url}/${uniprot.xsd.schema.name}</url>
<outputFileName>${uniprot.xsd.schema.name}</outputFileName>
<outputDirectory>${project.build.directory}/${uniprot.xsd.schema.download.location}</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
<!-- Build Java classes from schema files (XSD, DTD) using XJC tool -->
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>jaxb2-maven-plugin</artifactId>
<version>3.1.0</version>
<executions>
<!-- UNIPROT KB -->
<execution>
<id>uniprot-schema-generate</id>
<phase>generate-sources</phase>
<goals>
<goal>xjc</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${uniprot.auto.gen.classes.location}</outputDirectory>
<packageName>${uniprot.auto.package}</packageName>
<extension>true</extension>
<sources>
<source>${project.build.directory}/${uniprot.xsd.schema.download.location}/${uniprot.xsd.schema.name}</source>
</sources>
<xjbSources>
<xjbSource>src/main/resources/jaxb-bindings/uniprot.xjb</xjbSource>
</xjbSources>
</configuration>
</execution>
<!-- NCBI esummary.fcgi -->
<execution>
<id>ncbi-schema-generate</id>
<phase>generate-sources</phase>
<goals>
<goal>xjc</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${ncbi.auto.gen.classes.location}</outputDirectory>
<packageName>${ncbi.auto.package}</packageName>
<extension>true</extension>
<sources>
<source>${ncbi.xsd.esummary.schema.file}</source>
<source>${ncbi.xsd.efetch.schema.file}</source>
</sources>
</configuration>
</execution>
<!-- MeSH Descriptor Record -->
<execution>
<id>mesh-schema-generate</id>
<phase>generate-sources</phase>
<goals>
<goal>xjc</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/${mesh.auto.gen.classes.location}</outputDirectory>
<packageName>${mesh.auto.package}</packageName>
<externalEntityProcessing>true</externalEntityProcessing>
<!-- Indicate that we should use DTD input instead of XSDs -->
<sourceType>dtd</sourceType>
<!-- Define the directory where we should find the DTD file -->
<sources>
<source>src/main/resources/dtd-mesh</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>3.0.1</version>
</plugin>
</plugins>
</build>
</project>